When All You Thought You Knew Turns Out to be Wrong
by Queen Apolline
Summary: It has been six years since Loki's attack. It has been three years since Clint and Natasha, as well as Director Fury, were assassinated by Maria Hill. The Avengers have done all they could under the circumstances, living in the present and remembering the past. But when there are intruders in the Tower, their entire perspective is changed, and everything they thought they knew.
1. Chapter 1

**Disclaimer: I do not own the Avengers and I never will.**

**AN: This chapter is going to be relatively predictable from the summary, like the first chapter of a book. You know it's going to happen, the characters just don't yet.**

"Sir, I am detecting an intrusion in the lower levels," Jarvis announced. Tony froze from where he worked on his suits. "Are you positive?" he asked. "Who is it? Where are they? They managed to make it in? Where did they penetrate?" "There are two intruders," Jarvis reported. "One male and one female. They penetrated with relative ease at the secret entrance to the vents under the back dumpster."

"How did they even know about that?" Tony muttered. The vent had been installed specifically so that Clint and Natasha could make it in unnoticed if need be, but since the deadly duo had died three years before, no one had used it. All the Avengers, the original ones, at least, knew about it, but only Clint, Natasha, and Tony knew exactly where it was.

"I do not know, sir," Jarvis replied. "They appeared to know the code, though I am not sure if they actually did or remotely accessed it instead, but they were wearing gloves, so I was unable to scan their fingerprints." "Where are they now?" Tony asked again. "They are in Vent 69A7S, in Sector 13, and they appear to be headed for the Lower Nest," the AI told him.

"No one's been down there since Clint and Natasha died," Tony muttered. "Actually, sir, all the Avengers were there briefly, just to show Mr. Pym, Ms. Van Dyne, and Mr. Parker where and what it was, and what its meaning was to the Avengers," Jarvis corrected.

"What's down there that they could be after?" Tony asked, moving to his assembly pad and assembling one of the suits around him. "I am not sure, sir," the AI replied. "Agents Barton and Romanoff left their Nerf weaponry down there, as well as the materials for their full-size Paper Toss game, and other personal items."

"It's like they're walking on their graves," Tony muttered as the helmet closed over his face. "Jarvis, open the hatch." The AI complied, opening the hatch that was just wide enough for Tony to fly through in the Iron Man suit. That had been Clint's idea, as Tony was making the vents big enough for him to move through anyway.

As he flew, the memories returned, of the two master assassins in the three years after the First Battle of Manhattan. They were up to like, seventeen Battles of Manhattan by now. For some reason, supervillains with alien/robot/brainwashed soldiers/mutant animals/all the other stuff the Avengers had encountered just loved the place. While the two had been the last to take Tony up on his offer to live in Stark Towers, they explained they'd been planning on it from the start, but they had gone away to hide from Fury, and as soon as they'd returned, they'd been sicced on several different people who'd made their way on SHIELD's naughty list, one after another.

The other Avengers had quickly learned that not only were the agents so serious and cold all the time, but they were actually fun-loving pranksters who were capable of matching Tony in a prank war. The day that they had died…Avengers Tower had been draped in black for a year, and Tony had paid millions for an impressive monument to them to be set up in Central Park. It was always covered in flowers, many from the Avengers, but many from grateful visitors who remembered that the pair had saved the world more than a dozen times.

The day they had died…it had broken the Avengers' hearts. Before that, it had been the happiest time of their lives. Bruce and Betty were together again, and happily so, as Bruce had finally come to accept the Other Guy, Steve was finally fitting in with the 21st Century, Thor had been reunited with Jane and had married her the year before, and Clint and Natasha had announced their engagement at Tony and Pepper's wedding the week before. The newlyweds had still been on their honeymoon when they got the call.

It had been Steve who called them. "Clint and Natasha are dead," he had told them. "So is Director Fury. We identified the bodies ten minutes ago." "Who killed them?" Tony had demanded, already suiting up as Iron Man. "You won't believe it," Steve had responded, "but it was Maria." "Maria?" Pepper had gasped. "But she's so nice! She loves them like a sister!" "We're shocked too," Steve had replied. "You both need to get back to the Tower ASAP."

The Council had appointed John Ragel as the new Director of SHIELD. As a tribute to Director Fury, he was often called Director Rage, or just simply 'Rage.' At first glance, he appeared to be a no-nonsense man that could scare anyone into doing what he ordered, but the Avengers had soon discovered that Jack Ragel was a caring family man who was utterly devoted to his two daughters, Sofia and Anastasia. His wife had been murdered years before, and it was obvious that he still missed her.

"Should I notify the other Avengers?" Jarvis asked, breaking into Tony's thoughts. "Or Director Rage?" "Nah, I can handle it," he replied. "If something goes wrong, contact the others." The others. The Avengers. His team. After the loss of Clint and Natasha, they had recruited the married Drs. Hank Pym and Janet Van Dyne, aka Ant-Man and Wasp. Spiderman was a more recent recruit, but he merged with the team well, despite still being in high school and spending most of his days there. "ETA, Jarvis?" Tony asked.

"Thirty seconds, sir," the AI replied. Sure enough, in thirty seconds, he was landing in the Lower Nest, the highest point in the underground Avengers complex, Clint and Natasha's favorite haunt. He raised his repulsors. "Put your hands up and turn around," he ordered the duo in black. The two intruders ignored the first order, but turned around violently. Tony's eyes widened as he gasped. Their eye, skin, and hair color was different, but he knew who these two were. He flipped up his face mask.

"Clint? Natasha?"


	2. Chapter 2

At the sound of their names, they bolted. Natasha snatched something from the table as she ran past. She darted towards the vent first, followed closely by Clint, who grabbed a set of arrows. One was drawn and pointed at Tony before he could move. "Don't move," Clint ordered coldly.

Tony slowly put his hands up. He'd had arrows pointed at him before, and knew the proper way to respond. "Guys, I…" he began, but Natasha cut him off. "Shut it, Stark," she ordered. Tony blinked. "Since when am I Stark? I thought we were on a first-name basis, Natasha!" "We _were_," she hissed.

"Deactivate the suit," Clint ordered. "What's with you guys?" Tony asked, doing as they said and hitting the release switch. The armor clattered to the ground around him. "You come back _from the dead_ and all you can do is threaten me?" Tony asked in disbelief. "No explanation for where you've been the past three years, why you faked your deaths, no apologies for deserting us…nothing? You're just running in, grabbing your old gear, and running out?"

Clint's arrow lowered slightly as he asked, "What do you mean 'back from the dead'?" "Um, you were reported KIA three years ago," Tony replied. "KIA?" Natasha asked, looking very confused. "Yeah, killed in action, lost in combat, assassinated, killed, terminated…" Tony went on, before Natasha said, "Can it, Tony, we know what KIA means. But what do you mean _we _were reported KIA?"

Tony smiled and spread his arms. "There we are, back on a first-name basis!" "Stark," Clint growled. "Right," Tony said hastily, putting his arms down. "We were informed three years ago that you, Legolas, you, Red, and our dear Pirate King were assassinated by Maria Hill. Steve, Bruce, Betty, Thor, and Jane all identified your bodies. You were dead, D-E-A-D dead."

Clint's eyes widened. "You're not working with him," he said. He lowered his bow and turned to Natasha. "Nat, they're not working for them! They can help us!" "It could be a ploy," she offered. Clint froze. "Right, Tony's the best liar besides us. But I don't think he is lying. It explains a lot of things." "Like us never seeing them," Natasha said in obvious realization. "Right, or the time that Fury hacked the mainframe at…" "Of course!" Natasha exclaimed.

Tony raised his hand and said, "Um, genius here, and I haven't the slightest idea what you're talking about." "Maria was framed, Tony," Natasha explained. "But she confessed!" Tony replied "She confessed under SHIELD interrogation!" "A "specialty" interrogation?" Clint questioned. Tony frowned and looked up, trying to think. "Yeah, that's what Rage called it."

"Rage?" the two former SHIELD agents asked in unison. "Yeah, Director John Ragel, we call him Jack Rage. He was appointed by the Council right after Fury was killed. Wait, don't tell me that the Pirate King is alive too?" The pair grinned, reminding Tony of when they pulled their greatest prank that had one them the prank war of 2014. "Not only is he alive, he's living up to his name," Clint replied.

"But Ragel…he's bad news," Natasha cautioned. Clint's face fell. "Right. He's been hunting us for three years." "Hunting you?" Tony asked in confusion. "Why?" "Because Ragel, under the Council's orders, ordered our deaths," Clint replied grimly.

"I don't understand," Tony said. Clint and Natasha exchanged looks, having one of their famous "silent conversations," and then turned back to Tony. "Assemble the Avengers," Natasha said, also grim. "We don't want to have to explain this twice."

"Jarvis?" Tony asked as he reassembled his armor around him. "Done, sir," the AI replied. "My I suggest you three convene in Mr. Stark's lab first? And I would like to be the first to extend my warmest greetings in regards to your return, Agents Barton and Romanoff." "Not agents anymore," Clint said, "but we sure as hell do more than any of the actual SHIELD agents do in defense of the world."

"Hey, that reminds me," Tony said. "Did you two ever tie the knot?" They shook their heads simultaneously. "We couldn't leave a paper trail," Natasha said. "So you've been engaged for three years now? Ugh, that's longer than Pepper made me wait!" Tony replied. "Hey, Robin Hood. Race you to my lab."

Clint smirked, and Tony could see the daredevil that still resided in there. "You're on," he replied cockily.

After a few minutes of furious racing through the air vents, they simultaneously arrived in Tony's lab…only to find Natasha already sitting there. "How did you…" Tony began, only to be interrupted by the spy saying, "I took the elevator." "I thought you were supposed to be the genius, Tony," Clint jeered. "Can it, Katniss," the billionaire grumbled as his suit was disassembled properly, again revealing his t-shirt and jeans.

"You ready to go face the Avengers?" he asked the pair. They exchanged glances and simultaneously said, "Nope." Tony looked at them again, and noticed their distinctly wrong appearances. "How fast can you change all those colors there, 'cause you'll look a lot better to our new members if they can recognize you."

"Got any laundry detergent?" Natasha asked. Tony tossed her a bottle from his desk. "Why is that even in here?" Clint asked in disbelief. Tony shrugged. "Pepper wanted me to invent something to get out all the stains that end up in my clothes. Make it quick, will you? Peter's a teenager, and therefore very impatient. And I'm not sure how long I can stall."

"Relax, Stark, we've got it all under control," Clint replied, already removing the color from his hair and skin. "Shoo, Tony," Natasha said. "Go stall. See you in a few minutes."


End file.
